John Reed makes the case against having a large surface navy. His arguments against a Marine Corps that exists to make amphibious assaults in the same article (e.g. D-Day was an Army operation and the Marines weren't terribly good at amphibious assault in WWII) are non-trivial.
I think that there is a place for a surface navy, but his basic point is right. For a great many purposes that the Navy was invented to serve and is still tasked with carrying out, the Navy is a poor tool, and surface ships are sitting ducks against a great many opponents.
I think he does underestimate how many potential adversaries are third rate powers against whom Naval based aviation is powerful and useful tool, in a world where U.S. land bases are often distant. I also think that he overstates how much of the Navy's resources are devoted to anything other than submarine and Naval aviation missions in a carrier group/assault ship group dominated force. And, I think he underestimates one of the biggest vulnerabilities of the naval force, which is the low profile and highly vunerable sealift force.